Communication

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Load Expression Data

## [1] "study: brca_tcga_pub2015"
## [1] "case: brca_tcga_pub2015_all"
## [1] "profile: brca_tcga_pub2015_rna_seq_v2_mrna_median_Zscores"

Overview of Expression Data

## [1] "set outliers with expression > 6 to 6"
## [1] "num ourliers before capping:" "14"
## [1] "num ourliers after capping:" "0"

Load Clinical Data

## 
## Others   TNBC 
##    621     51

Plotting

TNBC

## [1] "Number of samples for TNBC"
## 
## Others   TNBC 
##    621     51 
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Others"       "TNBC"

ER_STATUS_BY_IHC

## [1] "Number of samples for ER_STATUS_BY_IHC"
## 
## Indeterminate      Negative      Positive 
##             2           175           601 
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive"     "Negative"

HER2_FISH_STATUS

## [1] "Number of samples for HER2_FISH_STATUS"
## 
## Indeterminate      Negative      Positive 
##             3           247            60 
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive"     "Negative"

PR_STATUS_BY_IHC

## [1] "Number of samples for PR_STATUS_BY_IHC"
## 
## Indeterminate      Negative      Positive 
##             4           251           522 
## [1] "Welch's t.test was used for p-value calculation"
## [1] "comparison: " "Positive"     "Negative"

Multiple Groups

TUMOR_STAGE

## [1] "Passed Levene's test(data not shown), perform ANOVA"
## [1] "Number of samples for AJCC_PATHOLOGIC_TUMOR_STAGE"
## 
##    I   IA   IB   II  IIA  IIB  III IIIA IIIB IIIC   IV    X 
##   75   60    5    3  269  190    2  112   22   48   13   10
## [1] "Welch t.test was used for p-value calculation to add * to the plot"
## [1] "ref is  I"

## [1] "ANOVA: not significant"
## [1] "Pair-wise comparisons: some significant pair-wise comparisons at the p-value level, at p.adj (holm) no comparison is significant"
##        .y. group1 group2           p p.adj p.format p.signif method
## 1   SEPHS2    IIA     IB 0.037326351  1.00   0.0373        * T-test
## 2   SEPHS2    IIB     IB 0.041083736  1.00   0.0411        * T-test
## 3   SEPHS2   IIIA     IB 0.020917058  1.00   0.0209        * T-test
## 4   SEPHS2     IV     IB 0.017876938  1.00   0.0179        * T-test
## 5   SEPHS2     IB   IIIB 0.026430262  1.00   0.0264        * T-test
## 6  SLC7A11      I    IIA 0.034594351  1.00   0.0346        * T-test
## 7  SLC7A11    IIA     IA 0.029578456  1.00   0.0296        * T-test
## 8  SLC7A11    IIA     IV 0.007058173  0.47   0.0071       ** T-test
## 9  SLC7A11    IIA      X 0.027349097  1.00   0.0273        * T-test
## 10 SLC7A11    IIA    III 0.022970266  1.00   0.0230        * T-test
## 11 SLC7A11   IIIB    III 0.035691849  1.00   0.0357        * T-test

CANCER_TYPE_DETAILED

## [1] "Levene's test failed, ANOVA assumption not met, only perform pair-wise Welch's T.test"
## [1] "Number of samples for CANCER_TYPE_DETAILED"
## 
##          Breast Invasive Ductal Carcinoma 
##                                       490 
##         Breast Invasive Lobular Carcinoma 
##                                       127 
## Breast Mixed Ductal and Lobular Carcinoma 
##                                        88 
##                 Invasive Breast Carcinoma 
##                                       113
## [1] "Welch's t.test was used for p-value calculation"
## [1] "Welch t.test was used for p-value calculation to add * to the plot"
## [1] "ref is  Breast Invasive Lobular Carcinoma"

## [1] "Pair-wise comparisons: all significant pair-wise comparisons at the p-value level listed, at p.adj (holm) some comparison is significant"
##        .y.                            group1
## 1     PSTK  Breast Invasive Ductal Carcinoma
## 2     SCLY Breast Invasive Lobular Carcinoma
## 3   SEPHS2         Invasive Breast Carcinoma
## 4   SEPHS2  Breast Invasive Ductal Carcinoma
## 5   SEPHS2 Breast Invasive Lobular Carcinoma
## 6  SEPSECS         Invasive Breast Carcinoma
## 7  SEPSECS         Invasive Breast Carcinoma
## 8  SEPSECS  Breast Invasive Ductal Carcinoma
## 9  SEPSECS  Breast Invasive Ductal Carcinoma
## 10 SLC7A11         Invasive Breast Carcinoma
## 11 SLC7A11  Breast Invasive Ductal Carcinoma
## 12 SLC7A11 Breast Invasive Lobular Carcinoma
##                                       group2            p   p.adj p.format
## 1  Breast Mixed Ductal and Lobular Carcinoma 1.648492e-02 9.9e-02  0.01648
## 2  Breast Mixed Ductal and Lobular Carcinoma 2.104185e-02 1.3e-01  0.02104
## 3          Breast Invasive Lobular Carcinoma 1.063428e-04 4.3e-04  0.00011
## 4          Breast Invasive Lobular Carcinoma 1.606515e-18 9.6e-18  < 2e-16
## 5  Breast Mixed Ductal and Lobular Carcinoma 2.394450e-05 1.2e-04  2.4e-05
## 6          Breast Invasive Lobular Carcinoma 4.158010e-02 1.2e-01  0.04158
## 7  Breast Mixed Ductal and Lobular Carcinoma 6.986600e-03 2.8e-02  0.00699
## 8          Breast Invasive Lobular Carcinoma 2.106862e-03 1.1e-02  0.00211
## 9  Breast Mixed Ductal and Lobular Carcinoma 7.956582e-04 4.8e-03  0.00080
## 10         Breast Invasive Lobular Carcinoma 2.227005e-02 8.9e-02  0.02227
## 11         Breast Invasive Lobular Carcinoma 8.874273e-06 5.3e-05  8.9e-06
## 12 Breast Mixed Ductal and Lobular Carcinoma 1.537631e-02 7.7e-02  0.01538
##    p.signif method
## 1         * T-test
## 2         * T-test
## 3       *** T-test
## 4      **** T-test
## 5      **** T-test
## 6         * T-test
## 7        ** T-test
## 8        ** T-test
## 9       *** T-test
## 10        * T-test
## 11     **** T-test
## 12        * T-test